RetrogeneDB ID: retro_ogar_2080

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873589.1:780137..781511(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ZKSCAN2
• Ensembl ID: ENSOGAG00000009286
• Aliases: None
• Description: zinc finger with KRAB and SCAN domains 2 [Source:HGNC Symbol;Acc:25677]

Sequence

>retro_ogar_2080
TCTGAGGCTTTTCGCAAATGCTTCAGGCAATTCTGTTATGAGGATGTGACCGGATCCCATTAAGGTTTTAGTAAACTCTG
GGAACTTTGCTGCTGGTGGCTGAAGCCAGAAATGCGTTCCAAGGAGCAGATACTTGAACTGCTGGTGATTAAGCAGTTTC
TCACCATTTTACCCGAGAATATTCAGGCTTGGGCACAGAAGCAGTGTCCAGAAAGTGGAGAGGAGGTGGTGGCATTGGTA
GTGCATTTGGAGAAAGAGACTGGAAAACTACGACATCAGGTCAGTAGTCCTGTACATACAAAGAAGAAAGCCCCCTTTGG
AGCAGCATGGGAGGTGTCAGAATTTCAGCCAGCCCAGGTGGAAACCCAAGCCAGGGTGATATCTCAGGAGGAAGCTGGAA
GCTACCACTCAGAACACCAGGAACATCTGAACCAAAAGAAAGAACATCAACCCTTACCCAAGAATGCTAGGCCTTCTCCC
TGGTTTCCTGCCCCTGCTGGTGAATGGAGCACCACAGATCAAGAAGTGATAACCTCACAACATCCCTTTGGGTCCCAGAA
ACCACTGAAAGATGTCCACATGACAAGAGGTTTCTCCTACAAAAGGAGTGTACATCAGATTCCTGCTCACAGAGGCCTCT
ACCAGGGTATCAGGAAGGAGAGTGTTGGGAACATGGTTTCCTTGGGTAGTACAGTGTCTATATCTAACAAGGCAACCCGG
TTGGACCAAAGAAAAGAGCCGTGGACTCTAGGTCTACATTCGTCCAATAAGAGGAGCATCCTGCGAAGCAACTACATCAA
GGAAAAGTCAGTTCATGCCATTCAGATCCCTGCAAGGAGTGCCGGGAAAGCATGGAGAGAGCAGCAACAGTGGGGTTTAG
AAGATGAAAAAATAGCAGGTGTGCACTGGAGCTATGAGGAAACTAAGACTTTTCTTGCAATTCTCAAAGAGTCTCGCTTT
TACGAAACTCTTCAGGCTTGTCCCCGAAATAGCCAGGTATATGGTGCTGTGGCTGAATGGTTGCGAGAATGTGGCTCCCT
CCGAACACCAGAACAGTGTCGGACTAAGTTCAAAAGTCTCCAAAAGAGCTATCGAAAAGTGAGAAATGGTCACATGCTAG
AACCCTGTGCCTTCTTTGAGGACATGGATGCATTGTTGAACCCTGCAGCCCATGCATCATCTGCTGATAAGCCAAAAGAG
ATGATGTCTTTGCCCAGAATGAAGAGAATTGGCATCACTGCTAAGGAACAGATCAGTTTGCTGGAAGAGGAGGAGGAAGC
TGCAGAAGATTCTGATGGTGATGAAATGGGCATTGAATTTATCCGCAAGTCTGAGACCTGTGGTGCCCCTGTCTTATTTC
AAAACCTGAGTGGT

Alignment

ORF - retro_ogar_2080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.2 %
• Parental protein coverage: 55.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEAFRKCFRQFCYEDVTGPHEAFSKLWELCCRWLKPEMRSKEQILELLVIEQFLTILPEKIQAWAQKQCP
          SEAFRKCFRQFCYEDVTG.H..FSKLWELCC.WLKPEMRSKEQILELLVI.QFLTILPE.IQAWAQKQCP
Retrocopy SEAFRKCFRQFCYEDVTGSH*GFSKLWELCCWWLKPEMRSKEQILELLVIKQFLTILPENIQAWAQKQCP

Parental  ESGEEAVALVVHLEKETGKLRHQVSSPVHTKKQAPFGAAWEVSQFQPAQVETQARVISQEEAGSHHSEHQ
          ESGEE.VALVVHLEKETGKLRHQVSSPVHTKK.APFGAAWEVS.FQPAQVETQARVISQEEAGS.HSEHQ
Retrocopy ESGEEVVALVVHLEKETGKLRHQVSSPVHTKKKAPFGAAWEVSEFQPAQVETQARVISQEEAGSYHSEHQ

Parental  EHLNQKKERQPLPKNARPSPWFPALAGGWSTTDQEVTTSRHPSGSQKPLKDVHMTRGYSYKKSVHQIPAH
          EHLNQKKE.QPLPKNARPSPWFPA.AG.WSTTDQEV.TS.HP.GSQKPLKDVHMTRG.SYK.SVHQIPAH
Retrocopy EHLNQKKEHQPLPKNARPSPWFPAPAGEWSTTDQEVITSQHPFGSQKPLKDVHMTRGFSYKRSVHQIPAH

Parental  RGLYQGIRKESVGNMVSLGSTVSISNKATRLDQRKEPWTLGLHSSNKRSILRSNYIKEKSIHAIQIPARS
          RGLYQGIRKESVGNMVSLGSTVSISNKATRLDQRKEPWTLGLHSSNKRSILRSNYIKEKS.HAIQIPARS
Retrocopy RGLYQGIRKESVGNMVSLGSTVSISNKATRLDQRKEPWTLGLHSSNKRSILRSNYIKEKSVHAIQIPARS

Parental  AGKAWREQQQWGLEDEKIAGVHWSYEETKTFLAILKESRFYETLQACPRNSQVYGAVAEWLRECGFLRTP
          AGKAWREQQQWGLEDEKIAGVHWSYEETKTFLAILKESRFYETLQACPRNSQVYGAVAEWLRECG.LRTP
Retrocopy AGKAWREQQQWGLEDEKIAGVHWSYEETKTFLAILKESRFYETLQACPRNSQVYGAVAEWLRECGSLRTP

Parental  EQCRTKFKSLQKSYRKVRNGHMLEPCAFFEDMDALLNPAAHASSADKPKEMMSLPRMKRIGITAKEQISL
          EQCRTKFKSLQKSYRKVRNGHMLEPCAFFEDMDALLNPAAHASSADKPKEMMSLPRMKRIGITAKEQISL
Retrocopy EQCRTKFKSLQKSYRKVRNGHMLEPCAFFEDMDALLNPAAHASSADKPKEMMSLPRMKRIGITAKEQISL

Parental  LEEEEEAAEDSDGDEMGIEFIRKSEIRGAPVLFQNLSG
          LEEEEEAAEDSDGDEMGIEFIRKSE..GAPVLFQNLSG
Retrocopy LEEEEEAAEDSDGDEMGIEFIRKSETCGAPVLFQNLSG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2080 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011162	1 retrocopy	retro_btau_270,
Otolemur garnettii	ENSOGAG00000009286	1 retrocopy	retro_ogar_2080 ,